- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] ff4232: Use ``detect_errors="exit_code"`` in ``__SET_METAD...
by GitHub 09 Nov '18

09 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ff4232b8b65b91969ae09f315b2955d44fcc4348 https://github.com/galaxyproject/galaxy/commit/ff4232b8b65b91969ae09f315b29… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M lib/galaxy/datatypes/set_metadata_tool.xml Log Message: ----------- Use ``detect_errors="exit_code"`` in ``__SET_METADATA__`` tool Commit: 5f2c785d66f76467dff23c6cc2edfcf9785e0bdd https://github.com/galaxyproject/galaxy/commit/5f2c785d66f76467dff23c6cc2ed… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M lib/galaxy/datatypes/set_metadata_tool.xml Log Message: ----------- Merge pull request #6989 from nsoranzo/set_metadata_detect_errors Use ``detect_errors="exit_code"`` in ``__SET_METADATA__`` tool Compare: https://github.com/galaxyproject/galaxy/compare/4960e08d2ab2...5f2c785d66f7 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 540636: Add utility function to create history entries
by GitHub 09 Nov '18

09 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 540636a241d61ae504037896b1e8071f83c35431 https://github.com/galaxyproject/galaxy/commit/540636a241d61ae504037896b1e8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M client/galaxy/scripts/layout/data.js Log Message: ----------- Add utility function to create history entries Commit: fca7bbc903932ed7330a319a2a695fd88e003fca https://github.com/galaxyproject/galaxy/commit/fca7bbc903932ed7330a319a2a69… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M client/galaxy/scripts/layout/data.js Log Message: ----------- Use auto as default extension type Commit: 8cf85232b489d16fe54de43b33d5b2e2928526ed https://github.com/galaxyproject/galaxy/commit/8cf85232b489d16fe54de43b33d5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-22 (Sat, 22 Sep 2018) Changed paths: M client/galaxy/scripts/layout/data.js Log Message: ----------- Use ? as default genome Commit: 4960e08d2ab285e8d02f8498d773a393198a7e01 https://github.com/galaxyproject/galaxy/commit/4960e08d2ab285e8d02f8498d773… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M client/galaxy/scripts/layout/data.js Log Message: ----------- Merge pull request #6693 from guerler/create_history_entry Add utility function to create history entries Compare: https://github.com/galaxyproject/galaxy/compare/eeca6f37a3b1...4960e08d2ab2 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/ansible-galaxy] 905248: Added report for current and max db version
by GitHub 09 Nov '18

09 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 90524880307b7285c77db1285f1fce0753653ea1 https://github.com/galaxyproject/ansible-galaxy/commit/90524880307b7285c77d… Author: eslerm <eslerm(a)umn.edu> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M tasks/database.yml Log Message: ----------- Added report for current and max db version Commit: 5506cd5d683e372de36a363e3da00b8eb52a09e0 https://github.com/galaxyproject/ansible-galaxy/commit/5506cd5d683e372de36a… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M tasks/database.yml Log Message: ----------- Merge pull request #35 from eslerm/database Added report for current and max database version Compare: https://github.com/galaxyproject/ansible-galaxy/compare/3853b8d5ee3a...5506… **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9842a3: Prevent errors when a library dataset has been pur...
by GitHub 09 Nov '18

09 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9842a378b12b216a670e3e108bc5ab8a580cc636 https://github.com/galaxyproject/galaxy/commit/9842a378b12b216a670e3e108bc5… Author: dpryan79 <dpryan79(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Prevent errors when a library dataset has been purged. Commit: eeca6f37a3b1c406f2389a32939b62269b682561 https://github.com/galaxyproject/galaxy/commit/eeca6f37a3b1c406f2389a32939b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #6784 from dpryan79/purged_library_datasets Prevent errors when a library dataset has been purged from disk Compare: https://github.com/galaxyproject/galaxy/compare/346b1bbfae56...eeca6f37a3b1 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 6bd251: Give all model objects with an id a __repr__ that ...
by GitHub 09 Nov '18

09 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6bd2513a35e24d9ac596eb77f66cc1f5896ec76e https://github.com/galaxyproject/galaxy/commit/6bd2513a35e24d9ac596eb77f66c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Give all model objects with an id a __repr__ that includes the id Commit: 414ce0a0eb18ad224d31136ad886079843814b66 https://github.com/galaxyproject/galaxy/commit/414ce0a0eb18ad224d31136ad886… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Use model.cached_id() instead of <obj>.id as per the tip from @jmchilton. Also, include the object's id (address) as with the default repr since it indicates whether an object is a different copy from another with the same id (database). Also catch any exceptions because failing to repr a model object could be pretty bad. Commit: 346b1bbfae5674a0212f626a5b9e4bd929fac889 https://github.com/galaxyproject/galaxy/commit/346b1bbfae5674a0212f626a5b9e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #6757 from natefoo/repr-model-objects Give all model objects with an id a __repr__ that includes the id Compare: https://github.com/galaxyproject/galaxy/compare/fdb571f57dad...346b1bbfae56 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] e8dbb8: Upgrade nodeenv's nodejs to 10.13.0 LTS, now that ...
by GitHub 09 Nov '18

09 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e8dbb8c58ab78a75044b5a5ebdd9f8dfb442aeac https://github.com/galaxyproject/galaxy/commit/e8dbb8c58ab78a75044b5a5ebdd9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Upgrade nodeenv's nodejs to 10.13.0 LTS, now that the client build works fine with v10 Commit: fdb571f57dadb3ab23a61cc369f766ef1e16fe12 https://github.com/galaxyproject/galaxy/commit/fdb571f57dadb3ab23a61cc369f7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #6991 from dannon/node_lts_upgrade Upgrade nodeenv's nodejs to 10.13.0 LTS Compare: https://github.com/galaxyproject/galaxy/compare/4e8922298010...fdb571f57dad **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 8c8261: Refactor cloud "upload">"get" api.
by GitHub 09 Nov '18

09 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8c826145d921b72731e611ce1b539372c477a368 https://github.com/galaxyproject/galaxy/commit/8c826145d921b72731e611ce1b53… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Refactor cloud "upload">"get" api. Commit: 6fc3aa35e8e7df9a4c2423b4e76bf90704f66559 https://github.com/galaxyproject/galaxy/commit/6fc3aa35e8e7df9a4c2423b4e76b… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Refactor cloud "upload">"get" in cloud manager. Commit: 74d1c1fcf809e940bbe9952e29d68f27f3f5af56 https://github.com/galaxyproject/galaxy/commit/74d1c1fcf809e940bbe9952e29d6… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update docstring following "upload">"get" refactoring. Commit: 4e8922298010deee8879862200989de1902aff48 https://github.com/galaxyproject/galaxy/commit/4e8922298010deee887986220098… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #6899 from VJalili/refactor_cloud_upload Refactor cloud "Upload" > "Get" Compare: https://github.com/galaxyproject/galaxy/compare/a882ccc88b1b...4e8922298010 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 840e76: Use card styles
by GitHub 09 Nov '18

09 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 840e760877c1f232603695d9c9099a8a309957c0 https://github.com/galaxyproject/galaxy/commit/840e760877c1f232603695d9c909… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Use card styles Commit: 58a1b4589250866d2de6ffdd2213232cb0d7c9cb https://github.com/galaxyproject/galaxy/commit/58a1b4589250866d2de6ffdd2213… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/style/scss/base.scss Log Message: ----------- Style revision workflow editor Commit: 2ef314ccd0e10d88ce1f4d1d52220c5cc5c51bc2 https://github.com/galaxyproject/galaxy/commit/2ef314ccd0e10d88ce1f4d1d5222… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: R client/galaxy/images/workflow_circle_drag.png R client/galaxy/images/workflow_circle_green.png R client/galaxy/images/workflow_circle_open.png M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/style/scss/base.scss Log Message: ----------- Remove legacy png files for workflow editor Commit: 656433f42802a92ce0fae086d7863b66ac8c4c12 https://github.com/galaxyproject/galaxy/commit/656433f42802a92ce0fae086d786… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: R client/galaxy/images/fugue/asterisk-small-outline.png R client/galaxy/images/fugue/asterisk-small-yellow.png R client/galaxy/images/fugue/asterisk-small.png M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/style/scss/base.scss Log Message: ----------- Replace asterisk png for marked terminal marking with fontawesome icon Commit: ba2dc44d9db3e9a0881c65e2358cb233c6683a8d https://github.com/galaxyproject/galaxy/commit/ba2dc44d9db3e9a0881c65e2358c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/style/scss/base.scss Log Message: ----------- Use icon instead of i as tag for terminal icons Commit: 64da2ca1f4794befc7ab8634fac63b6b393936b3 https://github.com/galaxyproject/galaxy/commit/64da2ca1f4794befc7ab8634fac6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Remove fixed icon height Commit: 9d559753af9c756e90154c11b6c286bbeb593077 https://github.com/galaxyproject/galaxy/commit/9d559753af9c756e90154c11b6c2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/library.scss M client/galaxy/style/scss/list-item.scss M client/galaxy/style/scss/ui/icon-btn.scss Log Message: ----------- Replace custom maroon highlighting by brand color Commit: a61017dbc70479d73f6ca944f7f2b1ab793e3df3 https://github.com/galaxyproject/galaxy/commit/a61017dbc70479d73f6ca944f7f2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Use panel color for module header backgrounds Commit: fbf514d2a022a02e3f1cc763451981ff6f73ddb9 https://github.com/galaxyproject/galaxy/commit/fbf514d2a022a02e3f1cc7634519… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Add editor background color to theme file Commit: 5506acc2f709954aa64a51b85912b8a90e33bfd2 https://github.com/galaxyproject/galaxy/commit/5506acc2f709954aa64a51b85912… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Revise workflow editor overview panel Commit: dc9c34bef3487e899d5cbeeb7afa1109618a0c64 https://github.com/galaxyproject/galaxy/commit/dc9c34bef3487e899d5cbeeb7afa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/style/scss/base.scss Log Message: ----------- Revise connector deletion option, remove from body and move to node, improve css specificity Commit: 6a9437b5c39d3ab554885c4cfe5f2cb926dfe6e3 https://github.com/galaxyproject/galaxy/commit/6a9437b5c39d3ab554885c4cfe5f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Remove unused z-index, previously used for global dom node features Commit: 3379d3e98116f9904f72076db4c46beb1ae614e1 https://github.com/galaxyproject/galaxy/commit/3379d3e98116f9904f72076db4c4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M client/galaxy/scripts/layout/panel.js M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move style spec for panel buttons from mako to scss file, revise editor workflow title Commit: 302a16da00d2c3c31a07160bbfe8d94552bce0a4 https://github.com/galaxyproject/galaxy/commit/302a16da00d2c3c31a07160bbfe8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js Log Message: ----------- Fix qunit test color Commit: e6faaa427e2a9f01540429d949d8b978961a09bc https://github.com/galaxyproject/galaxy/commit/e6faaa427e2a9f01540429d949d8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js Log Message: ----------- Remove hard-coded style attribute from drag terminal Commit: 8ea6fff8d82ad230689cf2fd47e39c8e9b158b47 https://github.com/galaxyproject/galaxy/commit/8ea6fff8d82ad230689cf2fd47e3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M test/galaxy_selenium/navigation.yml Log Message: ----------- Fix selenium tests Commit: 99ca7939acec122a252c15733ff0da18814f880b https://github.com/galaxyproject/galaxy/commit/99ca7939acec122a252c15733ff0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Improve delete option alignment Commit: c95cc50282873761f83ae930bcb3f652922a690a https://github.com/galaxyproject/galaxy/commit/c95cc50282873761f83ae930bcb3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M .ci/jenkins/api/run_tests.sh M .ci/jenkins/framework/run_tests.sh M .ci/jenkins/integration/run_tests.sh M .ci/jenkins/main-tools/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .ci/jenkins/toolshed/run_tests.sh M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/libs/jquery.custom.js R client/galaxy/scripts/libs/jquery/jstorage.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/utils/metrics-logger.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/plugins/visualizations/common/templates/chart_entry_point.mako M doc/schema_template.md M doc/source/admin/jobs.md M lib/galaxy/datatypes/text.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/controllers/history.py M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- Merge branch 'dev' into workflow_style_2 Commit: a882ccc88b1b79cd78550161b40507a9da1b2075 https://github.com/galaxyproject/galaxy/commit/a882ccc88b1b79cd78550161b405… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/style/scss/base.scss Log Message: ----------- Client format Compare: https://github.com/galaxyproject/galaxy/compare/588dbfaa68d5...a882ccc88b1b **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] eb8916: Trim whitespace from data manager conf paths
by GitHub 09 Nov '18

09 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eb8916e93fd690631fcaf588a1d17ecf2f3d67db https://github.com/galaxyproject/galaxy/commit/eb8916e93fd690631fcaf588a1d1… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-09-08 (Sat, 08 Sep 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Trim whitespace from data manager conf paths The templates used for `<target>` and `<value_translation>` tags should be `.strip()` to make it easier to write sophisticated templates that still yield a single line. Commit: 588dbfaa68d5a39cd7a153b785f0dcb097bb39af https://github.com/galaxyproject/galaxy/commit/588dbfaa68d5a39cd7a153b785f0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Merge pull request #6682 from pvanheus/patch-5 Trim whitespace from data manager conf paths Compare: https://github.com/galaxyproject/galaxy/compare/fc87b19a1cdd...588dbfaa68d5 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 4add47: Replaced jStorage with store
by GitHub 09 Nov '18

09 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4add47b2642a9719351e417e016945eadd3cfd27 https://github.com/galaxyproject/galaxy/commit/4add47b2642a9719351e417e0169… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/libs/jquery.custom.js R client/galaxy/scripts/libs/jquery/jstorage.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/utils/metrics-logger.js M client/package.json M client/webpack.config.js M client/yarn.lock M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- Replaced jStorage with store Commit: fc66e88642d0d1c00c24b4507a317ca3c65dd348 https://github.com/galaxyproject/galaxy/commit/fc66e88642d0d1c00c24b4507a31… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M client/galaxy/scripts/libs/jquery.custom.js Log Message: ----------- Update jquery.custom.js Committing just to make the tests run again. Commit: f8d50824acf2a8f6cf6bd324f5607ebb99379629 https://github.com/galaxyproject/galaxy/commit/f8d50824acf2a8f6cf6bd324f560… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Removed debugger statement Commit: a64fa50c760484d5710588c89600a4597caba10c https://github.com/galaxyproject/galaxy/commit/a64fa50c760484d5710588c89600… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M client/galaxy/scripts/libs/jquery.custom.js Log Message: ----------- Merge branch 'replace_jstorage' of https://github.com/Nerdinacan/galaxy into replace_jstorage Commit: fc87b19a1cdd14965ed85fe750b17698bea30ebd https://github.com/galaxyproject/galaxy/commit/fc87b19a1cdd14965ed85fe750b1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/libs/jquery.custom.js R client/galaxy/scripts/libs/jquery/jstorage.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/utils/metrics-logger.js M client/package.json M client/webpack.config.js M client/yarn.lock M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- Merge pull request #6994 from Nerdinacan/replace_jstorage Replaced jStorage with store Compare: https://github.com/galaxyproject/galaxy/compare/46126cda0990...fc87b19a1cdd **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 03794c: Fix broken links on Job Configuration page
by GitHub 08 Nov '18

08 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 03794ce21aabe40bc942eed7ef3442ec9b0960b6 https://github.com/galaxyproject/galaxy/commit/03794ce21aabe40bc942eed7ef34… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M doc/source/admin/jobs.md Log Message: ----------- Fix broken links on Job Configuration page Commit: 46126cda099095c70079f3f297201f01e1350df1 https://github.com/galaxyproject/galaxy/commit/46126cda099095c70079f3f29720… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M doc/source/admin/jobs.md Log Message: ----------- Merge pull request #6992 from ic4f/dev Fix broken links on Job Configuration page (documentation) Compare: https://github.com/galaxyproject/galaxy/compare/7966ca5a95d5...46126cda0990 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ebb6e7: Don't mount external /tmp for tests.
by GitHub 08 Nov '18

08 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ebb6e78f0d86555be0b53d635f076cae3d945eb2 https://github.com/galaxyproject/galaxy/commit/ebb6e78f0d86555be0b53d635f07… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M .ci/jenkins/api/run_tests.sh M .ci/jenkins/framework/run_tests.sh M .ci/jenkins/integration/run_tests.sh M .ci/jenkins/main-tools/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .ci/jenkins/toolshed/run_tests.sh Log Message: ----------- Don't mount external /tmp for tests. Nate wants the file busy errors back ;). Commit: 7966ca5a95d57ee986621bd180e3ff8858e1624c https://github.com/galaxyproject/galaxy/commit/7966ca5a95d57ee986621bd180e3… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M .ci/jenkins/api/run_tests.sh M .ci/jenkins/framework/run_tests.sh M .ci/jenkins/integration/run_tests.sh M .ci/jenkins/main-tools/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .ci/jenkins/toolshed/run_tests.sh Log Message: ----------- Merge pull request #6990 from jmchilton/skip_mounting_external_tmp_in_ci_tests Don't mount external /tmp for tests. Compare: https://github.com/galaxyproject/galaxy/compare/f9a84b0ffe36...7966ca5a95d5 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 258ada: Added a metadata element to the biom1 datatype
by GitHub 08 Nov '18

08 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 258ada862ece5a06b8a86530cd9f22c355a80ac1 https://github.com/galaxyproject/galaxy/commit/258ada862ece5a06b8a86530cd9f… Author: Slugger70 <slugger70(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Added a metadata element to the biom1 datatype Commit: 789f7b2d8dd72833e2c295535ca58fb9f46806b5 https://github.com/galaxyproject/galaxy/commit/789f7b2d8dd72833e2c295535ca5… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- As per review Co-Authored-By: Slugger70 <slugger70(a)gmail.com> Commit: fc53123a94c2ba625c1e6075e0e3a284bddf2d29 https://github.com/galaxyproject/galaxy/commit/fc53123a94c2ba625c1e6075e0e3… Author: Slugger70 <slugger70(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Changes as per review Commit: 9d9bc9e27269d347e87846374492ce4a5290dad1 https://github.com/galaxyproject/galaxy/commit/9d9bc9e27269d347e87846374492… Author: Slugger70 <slugger70(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Log Message: ----------- Made changes as per review Commit: 0bc6e35ad60a1f3b4e5db5691cc26fb67728d2bc https://github.com/galaxyproject/galaxy/commit/0bc6e35ad60a1f3b4e5db5691cc2… Author: Slugger70 <slugger70(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Minor alteration for flake8 Commit: 6dd098f747c89ba3494b64bb5a64dc078bb3d5db https://github.com/galaxyproject/galaxy/commit/6dd098f747c89ba3494b64bb5a64… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Simplify code Commit: f9a84b0ffe36a79df7c83d7fcca23efa30f07d89 https://github.com/galaxyproject/galaxy/commit/f9a84b0ffe36a79df7c83d7fcca2… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #6972 from Slugger70/biom_datatype_changes Added a metadata element to the biom1 datatype Compare: https://github.com/galaxyproject/galaxy/compare/e4c00af38d38...f9a84b0ffe36 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 0ecb4e: List tags as attribute of TestCollection
by GitHub 08 Nov '18

08 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0ecb4e7c595f7fb6cd6e648c4d770e1e97530424 https://github.com/galaxyproject/galaxy/commit/0ecb4e7c595f7fb6cd6e648c4d77… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- List tags as attribute of TestCollection Commit: bff5d51245f76bfc0bbe5b71237b3709d9ff7079 https://github.com/galaxyproject/galaxy/commit/bff5d51245f76bfc0bbe5b71237b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Use comma-separated instead of comma separated Commit: 5e098857e5dee703741e070e24a40235fb5deff2 https://github.com/galaxyproject/galaxy/commit/5e098857e5dee703741e070e24a4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M doc/schema_template.md Log Message: ----------- Display test collection input in documentation Commit: 4760a0ac0f48b106f9a1cee348deeccc223eb64a https://github.com/galaxyproject/galaxy/commit/4760a0ac0f48b106f9a1cee348de… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Fix recursion issue in gff_filter_by_feature_count Commit: 5e1fb9a7a2935fc3a3e599b6111157c91fe7b345 https://github.com/galaxyproject/galaxy/commit/5e1fb9a7a2935fc3a3e599b61111… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6983 from mvdbeek/schema_amamdment_tags_in_collection [18.09] List tags as attribute of TestCollection Commit: 45e475e19aa1988db2461c1d7fdf6135c02294d0 https://github.com/galaxyproject/galaxy/commit/45e475e19aa1988db2461c1d7fdf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Merge pull request #6986 from nsoranzo/release_18.05_backport_2d36e8955e020958334088d6ba5853c1027d8b75 [18.05] Backport commit 2d36e8955e020958334088d6ba5853c1027d8b75 Commit: f85afad9655b970f3af895a8dfafc0b8e301c705 https://github.com/galaxyproject/galaxy/commit/f85afad9655b970f3af895a8dfaf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-08 (Thu, 08 Nov 2018) Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: e4c00af38d387ee860050916e6b2c28f57b2fd4e https://github.com/galaxyproject/galaxy/commit/e4c00af38d387ee860050916e6b2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d28ce7686d12...e4c00af38d38 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 4760a0: Fix recursion issue in gff_filter_by_feature_count
by GitHub 08 Nov '18

08 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 4760a0ac0f48b106f9a1cee348deeccc223eb64a https://github.com/galaxyproject/galaxy/commit/4760a0ac0f48b106f9a1cee348de… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Fix recursion issue in gff_filter_by_feature_count Commit: 45e475e19aa1988db2461c1d7fdf6135c02294d0 https://github.com/galaxyproject/galaxy/commit/45e475e19aa1988db2461c1d7fdf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Merge pull request #6986 from nsoranzo/release_18.05_backport_2d36e8955e020958334088d6ba5853c1027d8b75 [18.05] Backport commit 2d36e8955e020958334088d6ba5853c1027d8b75 Commit: f85afad9655b970f3af895a8dfafc0b8e301c705 https://github.com/galaxyproject/galaxy/commit/f85afad9655b970f3af895a8dfaf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-08 (Thu, 08 Nov 2018) Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/5e1fb9a7a293...f85afad9655b **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ccb1e0: In enqueue, always set an object_store_id if one i...
by GitHub 08 Nov '18

08 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: ccb1e08000759184b2ebc4d26b8e88ebe9b4c9c4 https://github.com/galaxyproject/galaxy/commit/ccb1e08000759184b2ebc4d26b8e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- In enqueue, always set an object_store_id if one isn't set. Tool actions other than the regular tool action (such as the upload ones) might not set an object store id even in the legacy mode. Commit: dc9128213fbf4fd1d479fc94ace5b2416a5face5 https://github.com/galaxyproject/galaxy/commit/dc9128213fbf4fd1d479fc94ace5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Fix traceback when starting under Python3 with ``galaxy.ini`` Update `paste` requirement to 3.0.4 to include: https://github.com/cdent/paste/pull/14 to fix the following traceback: ``` Starting server in PID 6792. Traceback (most recent call last): File "./scripts/paster.py", line 27, in <module> serve.run() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1055, in run invoke(command, command_name, options, args[1:]) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1061, in invoke exit_code = runner.run(args) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 226, in run result = self.command() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 676, in command serve() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 653, in serve server(app) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 232, in server_wrapper **context.local_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 90, in fix_call val = callable(*args, **kw) File "/opt/galaxy/.venv3/lib/python3.5/site-packages/paste/httpserver.py", line 1358, in server_runner for name, value in kwargs.items(): RuntimeError: dictionary changed size during iteration galaxy.app DEBUG 2018-11-05 13:38:00,059 Shutting down ``` Commit: 9029b95e69795992ecf67f3ffdfa6384b52e1f3a https://github.com/galaxyproject/galaxy/commit/9029b95e69795992ecf67f3ffdfa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #6969 from jmchilton/ensure_better [18.09] In enqueue, always set an object_store_id if one isn't set. Commit: 6487d52d513b6351bd3e3e44e74e79c8f949919a https://github.com/galaxyproject/galaxy/commit/6487d52d513b6351bd3e3e44e74e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6978 from nsoranzo/release_18.09_paste [18.09] Fix traceback when starting under Python3 with ``galaxy.ini`` Commit: 0ecb4e7c595f7fb6cd6e648c4d770e1e97530424 https://github.com/galaxyproject/galaxy/commit/0ecb4e7c595f7fb6cd6e648c4d77… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- List tags as attribute of TestCollection Commit: bff5d51245f76bfc0bbe5b71237b3709d9ff7079 https://github.com/galaxyproject/galaxy/commit/bff5d51245f76bfc0bbe5b71237b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Use comma-separated instead of comma separated Commit: 5e098857e5dee703741e070e24a40235fb5deff2 https://github.com/galaxyproject/galaxy/commit/5e098857e5dee703741e070e24a4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M doc/schema_template.md Log Message: ----------- Display test collection input in documentation Commit: 5e1fb9a7a2935fc3a3e599b6111157c91fe7b345 https://github.com/galaxyproject/galaxy/commit/5e1fb9a7a2935fc3a3e599b61111… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6983 from mvdbeek/schema_amamdment_tags_in_collection [18.09] List tags as attribute of TestCollection Commit: 51498fc994f10d7c7bb71948b265f3c93c6ca7bf https://github.com/galaxyproject/galaxy/commit/51498fc994f10d7c7bb71948b265… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M doc/schema_template.md M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge branch 'release_18.09' Compare: https://github.com/galaxyproject/galaxy/compare/fefa132cd741...51498fc994f1 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/ansible-galaxy] ddda1d: Update deprecated syntax
by GitHub 08 Nov '18

08 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: ddda1d5a03e08a91f156da288a368b069398985b https://github.com/galaxyproject/ansible-galaxy/commit/ddda1d5a03e08a91f156… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M README.md Log Message: ----------- Update deprecated syntax Invoking "apt" only once while using a loop via squash_actions is deprecated. Use list of items as name value instead. Commit: 3853b8d5ee3a4a1830f7dd2f30208819afc996a2 https://github.com/galaxyproject/ansible-galaxy/commit/3853b8d5ee3a4a1830f7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M README.md Log Message: ----------- Merge pull request #41 from ic4f/master Update deprecated syntax Compare: https://github.com/galaxyproject/ansible-galaxy/compare/1043f1c3931e...3853… **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 0ecb4e: List tags as attribute of TestCollection
by GitHub 07 Nov '18

07 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 0ecb4e7c595f7fb6cd6e648c4d770e1e97530424 https://github.com/galaxyproject/galaxy/commit/0ecb4e7c595f7fb6cd6e648c4d77… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- List tags as attribute of TestCollection Commit: bff5d51245f76bfc0bbe5b71237b3709d9ff7079 https://github.com/galaxyproject/galaxy/commit/bff5d51245f76bfc0bbe5b71237b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Use comma-separated instead of comma separated Commit: 5e098857e5dee703741e070e24a40235fb5deff2 https://github.com/galaxyproject/galaxy/commit/5e098857e5dee703741e070e24a4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M doc/schema_template.md Log Message: ----------- Display test collection input in documentation Commit: 5e1fb9a7a2935fc3a3e599b6111157c91fe7b345 https://github.com/galaxyproject/galaxy/commit/5e1fb9a7a2935fc3a3e599b61111… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6983 from mvdbeek/schema_amamdment_tags_in_collection [18.09] List tags as attribute of TestCollection Compare: https://github.com/galaxyproject/galaxy/compare/6487d52d513b...5e1fb9a7a293 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] cd1a6b: Move disabled tool style from mako to scss
by GitHub 07 Nov '18

07 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cd1a6b2ef8f1169f39505bf67644100657b4a64c https://github.com/galaxyproject/galaxy/commit/cd1a6b2ef8f1169f39505bf67644… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move disabled tool style from mako to scss Commit: 551ac053dd8a5d75f53681a314e4aeed161c629f https://github.com/galaxyproject/galaxy/commit/551ac053dd8a5d75f53681a314e4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove unused post job action form styles Commit: 3e3021d6f3cbfa4871e6c8836a6ac051f9c3041d https://github.com/galaxyproject/galaxy/commit/3e3021d6f3cbfa4871e6c8836a6a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove title and row styles from mako to scss Commit: 6247955ebb0b3755057a5b41c58175a6effaeec8 https://github.com/galaxyproject/galaxy/commit/6247955ebb0b3755057a5b41c581… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move panel margins from mako to scss Commit: c7f65aee677fe5cc8c9322e99f5388e842191b39 https://github.com/galaxyproject/galaxy/commit/c7f65aee677fe5cc8c9322e99f53… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove custom body panel margins Commit: 1f82b33e704be5121c5c9b2eba4dfa59d8a586aa https://github.com/galaxyproject/galaxy/commit/1f82b33e704be5121c5c9b2eba4d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move ruler style to scss Commit: 496e353e86aef3868c68756ec0184fe38942ef0c https://github.com/galaxyproject/galaxy/commit/496e353e86aef3868c68756ec018… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move callout for hidden outputs to scss Commit: 5e0921cc9edd5ea0067b8da02bc119528eed2340 https://github.com/galaxyproject/galaxy/commit/5e0921cc9edd5ea0067b8da02bc1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Consolidate module step titles Commit: 4c2bc2222f5aadd102293cbd081b41511d15cd80 https://github.com/galaxyproject/galaxy/commit/4c2bc2222f5aadd102293cbd081b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove unused form-row-clear specification Commit: e9255599bd7de37ba57a6b72cad681e7c25a956a https://github.com/galaxyproject/galaxy/commit/e9255599bd7de37ba57a6b72cad6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove unused title row specification Commit: e0d891b2741f9e65c526d95bcb3c4474d8a8b9d0 https://github.com/galaxyproject/galaxy/commit/e0d891b2741f9e65c526d95bcb3c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move error highlighting to scss Commit: c01f7d2b63cc120cea419eaf06f2ef99879d0b99 https://github.com/galaxyproject/galaxy/commit/c01f7d2b63cc120cea419eaf06f2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move custom step margins to scss Commit: 6e41c8a404280e8bd13082b5ea6b7495da7002dd https://github.com/galaxyproject/galaxy/commit/6e41c8a404280e8bd13082b5ea6b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Fix callout style, currently global, attached to body Commit: ec97b380df757fb2c8282850a6b5178430d45ec5 https://github.com/galaxyproject/galaxy/commit/ec97b380df757fb2c8282850a6b5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove duplicate border highlighting for module forms Commit: 4417632cea7f90e21962a9f8f4d014644cf219f5 https://github.com/galaxyproject/galaxy/commit/4417632cea7f90e21962a9f8f4d0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Consolidate module representation specifications Commit: f19ac2d05270d06d7f1e5506471d53743506b733 https://github.com/galaxyproject/galaxy/commit/f19ac2d05270d06d7f1e5506471d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove unused panel button styles Commit: cfc4ed879997670c7963da095b85a06aea6f17ce https://github.com/galaxyproject/galaxy/commit/cfc4ed879997670c7963da095b85… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move callout button specification to scss Commit: 3fc6191f9562da97bd993816a7d0104046dbc8d7 https://github.com/galaxyproject/galaxy/commit/3fc6191f9562da97bd993816a7d0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove unused canvas area styles Commit: f0df34eacadf5d6f23bc4791d612352de6fe102c https://github.com/galaxyproject/galaxy/commit/f0df34eacadf5d6f23bc4791d612… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #6967 from guerler/workflow_style_1 Refactor workflow editor styles and move from mako to css Compare: https://github.com/galaxyproject/galaxy/compare/be87d2402d09...f0df34eacadf **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] dc9128: Fix traceback when starting under Python3 with ``g...
by GitHub 07 Nov '18

07 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dc9128213fbf4fd1d479fc94ace5b2416a5face5 https://github.com/galaxyproject/galaxy/commit/dc9128213fbf4fd1d479fc94ace5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Fix traceback when starting under Python3 with ``galaxy.ini`` Update `paste` requirement to 3.0.4 to include: https://github.com/cdent/paste/pull/14 to fix the following traceback: ``` Starting server in PID 6792. Traceback (most recent call last): File "./scripts/paster.py", line 27, in <module> serve.run() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1055, in run invoke(command, command_name, options, args[1:]) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1061, in invoke exit_code = runner.run(args) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 226, in run result = self.command() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 676, in command serve() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 653, in serve server(app) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 232, in server_wrapper **context.local_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 90, in fix_call val = callable(*args, **kw) File "/opt/galaxy/.venv3/lib/python3.5/site-packages/paste/httpserver.py", line 1358, in server_runner for name, value in kwargs.items(): RuntimeError: dictionary changed size during iteration galaxy.app DEBUG 2018-11-05 13:38:00,059 Shutting down ``` Commit: 6487d52d513b6351bd3e3e44e74e79c8f949919a https://github.com/galaxyproject/galaxy/commit/6487d52d513b6351bd3e3e44e74e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6978 from nsoranzo/release_18.09_paste [18.09] Fix traceback when starting under Python3 with ``galaxy.ini`` Commit: be87d2402d09cee0f2e43677f7073f7333876c94 https://github.com/galaxyproject/galaxy/commit/be87d2402d09cee0f2e43677f707… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/09186c991ae8...be87d2402d09 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] a8eb94: test/selenium_tests/test_library_contents.py
by GitHub 07 Nov '18

07 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a8eb9463a6778772b7c00cf3e80364cdb5956edd https://github.com/galaxyproject/galaxy/commit/a8eb9463a6778772b7c00cf3e803… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M test/selenium_tests/test_library_contents.py Log Message: ----------- test/selenium_tests/test_library_contents.py Commit: 10723c789f83f2a3ec9e4ba73ec3d08321d02ed3 https://github.com/galaxyproject/galaxy/commit/10723c789f83f2a3ec9e4ba73ec3… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M test/selenium_tests/test_library_contents.py Log Message: ----------- Added white space to pass linter Commit: 1b18e9ea2dcc403d44a972433c0f75c823107a8c https://github.com/galaxyproject/galaxy/commit/1b18e9ea2dcc403d44a972433c0f… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M test/selenium_tests/test_library_contents.py Log Message: ----------- More linting fun Commit: 09186c991ae88f9f4edf67f4ba98cc73286831b3 https://github.com/galaxyproject/galaxy/commit/09186c991ae88f9f4edf67f4ba98… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M test/selenium_tests/test_library_contents.py Log Message: ----------- Merge pull request #6982 from Nerdinacan/selenium_test_library_contents Update test/selenium_tests/test_library_contents.py Compare: https://github.com/galaxyproject/galaxy/compare/2f2153292b39...09186c991ae8 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 959e6f: Add a wrapper for the download-to-cloud tool.
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 959e6f0d55a7647ae096d996d91e18f8755ce2f2 https://github.com/galaxyproject/galaxy/commit/959e6f0d55a7647ae096d996d91e… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: A tools/cloud/download.xml Log Message: ----------- Add a wrapper for the download-to-cloud tool. Commit: 21602ba426ce2363f54529c0f3069b86ea163a50 https://github.com/galaxyproject/galaxy/commit/21602ba426ce2363f54529c0f306… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: A tools/cloud/download.py Log Message: ----------- Draft download-to-cloud tool. Commit: 90e879c5d773f79c2e0544ba9bb58ecdc1a6bc39 https://github.com/galaxyproject/galaxy/commit/90e879c5d773f79c2e0544ba9bb5… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M config/tool_conf.xml.main M config/tool_conf.xml.sample Log Message: ----------- Add entries in tool config samples pointing to the cloud download tool. Commit: 1d1b72999a0022644a22b99c5db10dc7acb4ba49 https://github.com/galaxyproject/galaxy/commit/1d1b72999a0022644a22b99c5db1… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Update cloud download manager to leverage the cloud download tool. Commit: 5567d5121f640c3b314a4be3a37cf3d1d470bd4b https://github.com/galaxyproject/galaxy/commit/5567d5121f640c3b314a4be3a37c… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Define two variables to store the cloud download tool name and version. Commit: 335c79cc972e6265bb764f69b5e0cf402ebd0d5a https://github.com/galaxyproject/galaxy/commit/335c79cc972e6265bb764f69b5e0… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Update xml file of the cloud download tool match new input setup. Commit: ad6a4334f42ca36b677adc0e93aa2c19f5ddd0c1 https://github.com/galaxyproject/galaxy/commit/ad6a4334f42ca36b677adc0e93aa… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Remove an unused import. Commit: 06371f3e84408124469e80f8b7a60b88f27275fa https://github.com/galaxyproject/galaxy/commit/06371f3e84408124469e80f8b7a6… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Refactor the _configure_provider method in cloud manager. Commit: 114b9bde8baccc6512ab7bfc5a9e142b1878adf5 https://github.com/galaxyproject/galaxy/commit/114b9bde8baccc6512ab7bfc5a9e… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Implement download function in the download-to-cloud tool. Commit: d6a9c202b103c65f77f8105ca9e4481cc8740167 https://github.com/galaxyproject/galaxy/commit/d6a9c202b103c65f77f8105ca9e4… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Update the argument parser in the download-to-cloud tool. Commit: f21e1b18eed88bbe5dd70d2831cd3ec6ea11578c https://github.com/galaxyproject/galaxy/commit/f21e1b18eed88bbe5dd70d2831cd… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Update the required arguments list in the download-to-cloud tool. Commit: 2ce272484a2fce1ab3bac3f16739d2e21a5b0cff https://github.com/galaxyproject/galaxy/commit/2ce272484a2fce1ab3bac3f16739… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Fix a bug in the config file of the Download-to-cloud tool. Commit: aa4f8d7cf9dcf9a65f8d90cdedaa5c5df0848c8c https://github.com/galaxyproject/galaxy/commit/aa4f8d7cf9dcf9a65f8d90cdedaa… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Add the download_to_cloud tool to GALAXY_LIB_TOOLS_UNVERSIONED array. Commit: 82d6a80d9e7f4f93ab65a3994d427fd67b2a30f7 https://github.com/galaxyproject/galaxy/commit/82d6a80d9e7f4f93ab65a3994d42… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M tools/cloud/download.py M tools/cloud/download.xml Log Message: ----------- Fix some bugs in the download-to-cloud tool and its wrapper. Commit: 2419c7107739a1894d8ce6be45d437abcfacc586 https://github.com/galaxyproject/galaxy/commit/2419c7107739a1894d8ce6be45d4… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix a bug in the cloud storage manager class. Commit: 880d0bcd69669b8f31f81b4c6e5328643d7fa35e https://github.com/galaxyproject/galaxy/commit/880d0bcd69669b8f31f81b4c6e53… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Cloud download skips deleted, purged, or non-OK datasets. Commit: 244638690c9b587c660f0ec65506cf496cec1f00 https://github.com/galaxyproject/galaxy/commit/244638690c9b587c660f0ec65506… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Write user credentials 2 a file & pass the path 2 file 2 download tool. Commit: 264796eddf7ee689c9a2746f3891453d032dff13 https://github.com/galaxyproject/galaxy/commit/264796eddf7ee689c9a2746f3891… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Cloud download tool now reads user credentials from a file. Commit: ac40ad52035fa3ef4856fa31c7281ca42b902f2f https://github.com/galaxyproject/galaxy/commit/ac40ad52035fa3ef4856fa31c728… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Delete the temporary credentials file after it is read. Commit: 72cd57d0114c4d90f7eb146247f0592bc36a8f99 https://github.com/galaxyproject/galaxy/commit/72cd57d0114c4d90f7eb146247f0… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py M tools/cloud/download.py M tools/cloud/download.xml Log Message: ----------- Refactor the `credentials` argument to `credentials_file`. Commit: ce5b05853aa86f054d5ed9e910c0bd06dee5a388 https://github.com/galaxyproject/galaxy/commit/ce5b05853aa86f054d5ed9e910c0… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M tools/cloud/download.py M tools/cloud/download.xml Log Message: ----------- Fix a bug naming variable/argument credentials_file (missing _file). Commit: 999f3b07aff9c65f46576314e5e241bc709ed440 https://github.com/galaxyproject/galaxy/commit/999f3b07aff9c65f46576314e5e2… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Convert bool in string type to Boolean type in Download-to-cloud tool. Commit: 0a2f838352634aba28fbd62f937024c9641ca59d https://github.com/galaxyproject/galaxy/commit/0a2f838352634aba28fbd62f9370… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Throw an err if the file of the dataset to be downloaded, doesn't exist. Commit: ffc8d42daf36451ebf1aebd95b4d4baaa63846fe https://github.com/galaxyproject/galaxy/commit/ffc8d42daf36451ebf1aebd95b4d… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Replace: (_ <- space) in HDA name when downloading to cloud, cos space is the delimiter for tools cli args. Commit: 35459b23c9c107e1c9f5820103ea4a025a071603 https://github.com/galaxyproject/galaxy/commit/35459b23c9c107e1c9f5820103ea… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Do not download if tool id is the download tool id. Commit: 94d14567847141ea18763870fd11b5109136b348 https://github.com/galaxyproject/galaxy/commit/94d14567847141ea18763870fd11… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix a bug determining the job created for downloading data to cloud. Commit: 2d6ed38e6fb7e580a5a3d15f4f7304e5eb5ded3e https://github.com/galaxyproject/galaxy/commit/2d6ed38e6fb7e580a5a3d15f4f73… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Cloud download API now returns the job id for each queued download job. Commit: cbca243eb70c1bcc2d4d523450b0bd7254f9a090 https://github.com/galaxyproject/galaxy/commit/cbca243eb70c1bcc2d4d523450b0… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Variable rename: uploaded -> downloaded. Commit: 275953be06073e83a9711f06d8fa22581ecb2d8b https://github.com/galaxyproject/galaxy/commit/275953be06073e83a9711f06d8fa… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update docs. Commit: 73b32652c3e02d9d8635cde9c11456116e084c2e https://github.com/galaxyproject/galaxy/commit/73b32652c3e02d9d8635cde9c114… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- In the Download tool xml, define provider param as a `select` type param Commit: df283962bb829b78da5fe4758e280430cdd2404e https://github.com/galaxyproject/galaxy/commit/df283962bb829b78da5fe4758e28… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.py M tools/cloud/download.xml Log Message: ----------- Replace `filename` with `input` in the download-to-cloud tool. Commit: 4b7615e98d18c2657c25ab8254ba5157f0bfbf06 https://github.com/galaxyproject/galaxy/commit/4b7615e98d18c2657c25ab8254ba… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.py M tools/cloud/download.xml Log Message: ----------- Refactor `input` back to `filename` as it causes issues in cloud API. Commit: b6196323d878c84bc9b4c744659035d152de0ccf https://github.com/galaxyproject/galaxy/commit/b6196323d878c84bc9b4c7446590… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Fix a bug in variable naming. Commit: fc8ae7eeefffc88124aeeb7b7076aa14e3d52506 https://github.com/galaxyproject/galaxy/commit/fc8ae7eeefffc88124aeeb7b7076… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Change the type of `overwrite_existing` key to boolean. Commit: a9dc89e5aa0e5e54c34748966859da00957e8df4 https://github.com/galaxyproject/galaxy/commit/a9dc89e5aa0e5e54c34748966859… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Download tool wrapper now takes provider-specific credentials. Commit: b60246c8e12fd469a2e248c1770e407639a832c2 https://github.com/galaxyproject/galaxy/commit/b60246c8e12fd469a2e248c1770e… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Pass credentials args based on the selected provider. Commit: f8ee1c161434d9cdc77422f4360fde52f76aef9f https://github.com/galaxyproject/galaxy/commit/f8ee1c161434d9cdc77422f4360f… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Update args list in the download.py. Commit: ef0dbb293165c8290833592927334eeb94867ac1 https://github.com/galaxyproject/galaxy/commit/ef0dbb293165c829083359292733… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Implement a args parser function in the download-to-cloud tool. Commit: 6c62cc57eb5ea337b0889a3f6bad6003557dc531 https://github.com/galaxyproject/galaxy/commit/6c62cc57eb5ea337b0889a3f6bad… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Refactor the parser function in the download-to-cloud tool. Commit: f2d1db9c23c10c8299ea2786e9420db17fc361df https://github.com/galaxyproject/galaxy/commit/f2d1db9c23c10c8299ea2786e942… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Refactor a variable. Commit: 4d83b83c22014580e373e36abb8b056ff6042b15 https://github.com/galaxyproject/galaxy/commit/4d83b83c22014580e373e36abb8b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-05 (Sun, 05 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Replace `provider` arg with connection, reflecting related conditional arg defined in the download-to-cloud tool wrapper. Commit: ab7741548475319006ef65d232b78f032f2a754b https://github.com/galaxyproject/galaxy/commit/ab7741548475319006ef65d232b7… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-05 (Sun, 05 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Instead of filename, cloud manager sends HDA to the download tool. Commit: 9d15ce4b21396b13e2a9a42373289451604a3525 https://github.com/galaxyproject/galaxy/commit/9d15ce4b21396b13e2a9a4237328… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-05 (Sun, 05 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Convert SUPPORTED_PROVIDERS to a dict reflecting their order in wrapper. Commit: 13aa6be72090dcd056f96b93db6c6cde896ee1fb https://github.com/galaxyproject/galaxy/commit/13aa6be72090dcd056f96b93db6c… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-05 (Sun, 05 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py M tools/cloud/download.xml Log Message: ----------- Add a comment. Commit: b4950a9678251ceb065add2f0cc3c666393c06e4 https://github.com/galaxyproject/galaxy/commit/b4950a9678251ceb065add2f0cc3… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-05 (Sun, 05 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- The Download-to-cloud tool now reads provider-specific credential args. Commit: 6c710ed85f444e3672c8aaf12e26c536c4060656 https://github.com/galaxyproject/galaxy/commit/6c710ed85f444e3672c8aaf12e26… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-05 (Sun, 05 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Fix a bug defining provider credentials in the download-to-cloud tool. Commit: 35eabd5543379702b92c439d7239e60f52f181f8 https://github.com/galaxyproject/galaxy/commit/35eabd5543379702b92c439d7239… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- In the download-to-cloud tool, set `object_label` to hda.name. Commit: 8502dc5b6138133319301ae926a4238031e7699f https://github.com/galaxyproject/galaxy/commit/8502dc5b6138133319301ae926a4… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- In the wrapper of download-to-cloud tool, hide `object_label`. Commit: 0aae0505951b7a0a33bebd263c100f624d50270e https://github.com/galaxyproject/galaxy/commit/0aae0505951b7a0a33bebd263c10… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- In the download-to-cloud tool, replace blank space in hda name with `_`. Commit: 1dd62afa7f16cee7b20c4b87ba705713d852da0f https://github.com/galaxyproject/galaxy/commit/1dd62afa7f16cee7b20c4b87ba70… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py M tools/cloud/download.py Log Message: ----------- Fix some lint issues. Commit: b5cbaaecbc3bc30e34c0700345eab0a6759cb7c1 https://github.com/galaxyproject/galaxy/commit/b5cbaaecbc3bc30e34c0700345ea… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Fix some lint issues. Commit: 9de5927b5bbe9c3baddef22ea89d85cf6d79cd50 https://github.com/galaxyproject/galaxy/commit/9de5927b5bbe9c3baddef22ea89d… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Rename the label of the output of the download-to-cloud. Commit: 2528c83bf2bc3483779fd509f5a8bab95e3e3690 https://github.com/galaxyproject/galaxy/commit/2528c83bf2bc3483779fd509f5a8… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Add docs to the download-to-cloud tool. Commit: 909c7a72d6fb9fce30844cee30909f017294fa89 https://github.com/galaxyproject/galaxy/commit/909c7a72d6fb9fce30844cee3090… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Add storage account and resource group as required args for Azure. Commit: 4d73ea6a6e61563d6f02787f7a851f5491345b58 https://github.com/galaxyproject/galaxy/commit/4d73ea6a6e61563d6f02787f7a85… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Add azure storage account & resource group to the download tool wrapper. Commit: 897d024ef7301403ec1ead14452493b2fda62bc1 https://github.com/galaxyproject/galaxy/commit/897d024ef7301403ec1ead144524… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Add Azure storage account and resource group to cloud manager. 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test/unit/workflows/test_workflow_progress.py M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/data_source/ucsc_tablebrowser_test.xml M tools/filters/bed_to_bigbed.xml M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.xml M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/sff_extractor.xml M tools/filters/tailWrapper.xml M tools/filters/uniq.xml M tools/filters/wc_gnu.xml M tools/filters/wig_to_bigwig.xml M tools/genomespace/genomespace_importer.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_split_by_species.xml M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/maf_to_interval.xml M tools/next_gen_conversion/solid2fastq.xml M tools/phenotype_association/ldtools.xml M tools/phenotype_association/ldtools_wrapper.sh M tools/phenotype_association/linkToGProfile.pl M tools/phenotype_association/linkToGProfile.xml M tools/phenotype_association/senatag.py M tools/plotting/boxplot.xml M tools/solid_tools/solid_qual_stats.py M tools/solid_tools/solid_qual_stats.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/gsummary.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into cloud_download_tool # Conflicts: # lib/galaxy/managers/cloud.py # lib/galaxy/webapps/galaxy/api/cloud.py Commit: 5c35813e302eab21db4f9c8e1e7c55e39339a9d3 https://github.com/galaxyproject/galaxy/commit/5c35813e302eab21db4f9c8e1e7c… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Replace credentials with authz_id in the payload of cloud download api. Commit: 8198b336bdbcf71264962b1eda7b5309ddb597ca https://github.com/galaxyproject/galaxy/commit/8198b336bdbcf71264962b1eda7b… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Use cloudauthz to get cloud credentials in cloud download manager. Commit: 08703ec87750e11bf41ceb1e68649670c6238c6a https://github.com/galaxyproject/galaxy/commit/08703ec87750e11bf41ceb1e6864… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Decode authz_id in cloud download api before sending it to the manager. Commit: 0e4045755f90f3d997e9200f036acc9408c32716 https://github.com/galaxyproject/galaxy/commit/0e4045755f90f3d997e9200f036a… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Replace the provider in cloud api with authz.provider. Commit: f3ebdae0ce05b1543839a15dd6000826e304d9c8 https://github.com/galaxyproject/galaxy/commit/f3ebdae0ce05b1543839a15dd600… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Fix incorrect argument and function naming in cloud api & manager. Commit: 5f8c0dfa342e12f10e06273a90c9034f96f617ca https://github.com/galaxyproject/galaxy/commit/5f8c0dfa342e12f10e06273a90c9… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-03 (Wed, 03 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/managers/cloud.py Log Message: ----------- Replace trans with sa_session and user_id in try_get_authz_config. Commit: 1babfdfda9ae7f95221b3992178fb25ee52e5161 https://github.com/galaxyproject/galaxy/commit/1babfdfda9ae7f95221b3992178f… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M client/README.md M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/upload/upload-settings.js M 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scripts/common_startup.sh M scripts/common_startup_functions.sh M static/style/blue/base.css M templates/galaxy_client_app.mako M templates/ind_share_base.mako M templates/show_params.mako M templates/user/info.mako M templates/user/register.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/history/share.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/common/repository_actions_menu.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/role/role.mako M templates/webapps/tool_shed/user/username.mako A test-data/safetar_with_symlink.tar A test-data/testdir.tar A test-data/unsafe.tar A test-data/unsafe.zip A test-data/unsafe_relative_symlink.tar M test/api/test_api_batch.py M test/api/test_dataset_collections.py M test/api/test_histories.py M test/api/test_jobs.py M test/api/test_pages.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/populators.py M test/base/workflow_fixtures.py R test/base/workflows_format_2/README.txt R test/base/workflows_format_2/__init__.py R test/base/workflows_format_2/converter.py R test/base/workflows_format_2/interface.py R test/base/workflows_format_2/main.py M test/functional/tools/disambiguate_cond.xml A test/functional/tools/identifier_in_conditional.xml M test/functional/tools/samples_tool_conf.xml M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py A test/unit/test_compression_util.py M test/unit/test_galaxy_mapping.py A test/unit/test_utils.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_toolbox_filters.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge and resolve conflicts. Commit: 9cf7cf6b1ea45478424bad81ffa2907bf12f8b01 https://github.com/galaxyproject/galaxy/commit/9cf7cf6b1ea45478424bad81ffa2… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- In the cloud download tool, accept credentials via a tmp file only. Commit: cf919d7befb7ef1c76e6afc710939e032da7dac4 https://github.com/galaxyproject/galaxy/commit/cf919d7befb7ef1c76e6afc71093… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Do not assert provider name in cloud download tool. Commit: 81eabec6e6517d9ef40b9880925bbcbffe95b6f6 https://github.com/galaxyproject/galaxy/commit/81eabec6e6517d9ef40b9880925b… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Update cloud download to adhere with cloudbridge v1 interface changes. Commit: b3a12919cab11f9a174b723cc2d686982a52924c https://github.com/galaxyproject/galaxy/commit/b3a12919cab11f9a174b723cc2d6… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Update download tool wrapper to leverage tmp credentials in tmp file. Commit: 68251722e346fc8fa4d9cec1860809688a5b4d74 https://github.com/galaxyproject/galaxy/commit/68251722e346fc8fa4d9cec18608… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- In authnz manager, user_id can be string & should be casted to int. Commit: 171b1dd26ea58f666e37672d73084b5ce4aa4dac https://github.com/galaxyproject/galaxy/commit/171b1dd26ea58f666e37672d7308… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Define a new func in authnz manager to write tmp cred. to a tmp file. Commit: 90f0a8615d927f1343bc1bc12519c96c04165280 https://github.com/galaxyproject/galaxy/commit/90f0a8615d927f1343bc1bc12519… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix a bug in calling get_cloud_access_credentials: missing args. Commit: 1b3855cc88cee647f70676f54c82c2174cae3f4d https://github.com/galaxyproject/galaxy/commit/1b3855cc88cee647f70676f54c82… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Inform user if a given decoded history to download from does not exist. Commit: 8d0b4e0c04cc003b02d9b9d5e089134f9b0bef64 https://github.com/galaxyproject/galaxy/commit/8d0b4e0c04cc003b02d9b9d5e089… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Pass authz_id from cloud download manager to the download tool wrapper. Commit: 4bcd3366ef5eabea4f89571c845b1f5667247ad9 https://github.com/galaxyproject/galaxy/commit/4bcd3366ef5eabea4f89571c845b… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Send bucket_name instead of bucket obj from cloud download mgr. to tool. Commit: e31c7768fb49966961fc8630672f3127b7df6e12 https://github.com/galaxyproject/galaxy/commit/e31c7768fb49966961fc8630672f… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Remove `connection` and `bucket` from cloud download manager. Commit: d9baf394d528586b44308f41cfa7041e3b8ab1d8 https://github.com/galaxyproject/galaxy/commit/d9baf394d528586b44308f41cfa7… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Cloud download tool: don't create cred. files if manager has provided. Commit: 5821fc1f1e932962f92bbabd9c7c3476e5770d61 https://github.com/galaxyproject/galaxy/commit/5821fc1f1e932962f92bbabd9c7c… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Leverage authnz manager to create and write tmp cred. to a tmp file. Commit: 9a8daa5e746203cd5fd537015aeaf53451f0a074 https://github.com/galaxyproject/galaxy/commit/9a8daa5e746203cd5fd537015aea… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Surround cloud download in try-catch and record failed datasets. Commit: 93a5a22b61f4cbea9a5def0928be134d6c25f5f4 https://github.com/galaxyproject/galaxy/commit/93a5a22b61f4cbea9a5def0928be… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Return & report a list of fails to create download job. Commit: 8cd1b0e118062555cdb7bc41c29b95f173deb5da https://github.com/galaxyproject/galaxy/commit/8cd1b0e118062555cdb7bc41c29b… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Remove hidden credentials_file arg from download tool wrapper. Commit: 1efa29419840425072d42db783afd456d7d126fe https://github.com/galaxyproject/galaxy/commit/1efa29419840425072d42db783af… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py M tools/cloud/download.xml Log Message: ----------- Encode and decode authnz id in download tool wrapper & manager. Commit: 9eabf5c6c61f18c0a91407c748e93c00e4d7022b https://github.com/galaxyproject/galaxy/commit/9eabf5c6c61f18c0a91407c748e9… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py M tools/cloud/download.xml Log Message: ----------- Only download tool wrapper creates tmp credentials tmp file. Commit: 8d68e8e5d33ca1c91c1f5b424d6045ece29946a4 https://github.com/galaxyproject/galaxy/commit/8d68e8e5d33ca1c91c1f5b424d60… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Remove unused imports from managers/cloud.py. Commit: 0061562bd8c112827c7cd0fd3a6ac4e8b92bd7ce https://github.com/galaxyproject/galaxy/commit/0061562bd8c112827c7cd0fd3a6a… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update cloud download API documentation. Commit: 7c599f8a8d762d5783e2534f91588e88e96b2510 https://github.com/galaxyproject/galaxy/commit/7c599f8a8d762d5783e2534f9158… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Provide more insights for errors occurring queuing cloud download jobs. Commit: 081e4eb96de77200322d4fb2998b950e8e789e0e https://github.com/galaxyproject/galaxy/commit/081e4eb96de77200322d4fb2998b… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update cloud download api docs w.r.t to updates to error reports. Commit: d316b9d7656c60a2888423790c9cf7ffd07dc666 https://github.com/galaxyproject/galaxy/commit/d316b9d7656c60a2888423790c9c… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Add docstring to get_cloud_access_credentials_in_file. Commit: 6504fe6ef1a15d379e8fad68dfe42d2e50dcb8e5 https://github.com/galaxyproject/galaxy/commit/6504fe6ef1a15d379e8fad68dfe4… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M tools/cloud/download.xml Log Message: ----------- Always pass user_id as int to authnz/managers so to avoid check & cast. Commit: 010c512855ea83a94a27d9ce754b053e6121c2ae https://github.com/galaxyproject/galaxy/commit/010c512855ea83a94a27d9ce754b… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Remove an extra space (lint issue). Commit: be34b7501829bdbadf13f502651ceb4d6697a7ab https://github.com/galaxyproject/galaxy/commit/be34b7501829bdbadf13f502651c… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Remove openstack from cloud manager's supported providers list. Commit: bd4023f521ed33cdaf9975e517b90cbe2b00e15b https://github.com/galaxyproject/galaxy/commit/bd4023f521ed33cdaf9975e517b9… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Add some logging to cloudauthz and cloud download api. Commit: 4305e2c56cc92a8cc67a29640897e92cc69a81e6 https://github.com/galaxyproject/galaxy/commit/4305e2c56cc92a8cc67a29640897… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Add some logging steps in the cloud download tool. Commit: 847f66340d1346fe7cd405b614c29c529ef7ddbb https://github.com/galaxyproject/galaxy/commit/847f66340d1346fe7cd405b614c2… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Remove a comment from download tool wrapper. Commit: 3ce2a3564799595fef08e5692a951757e853bf72 https://github.com/galaxyproject/galaxy/commit/3ce2a3564799595fef08e5692a95… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Update print func syntax in cloud download tool to adhere with py3 req. Commit: e943ec2bb48c6cbd693e0981d6134c4443f5ed70 https://github.com/galaxyproject/galaxy/commit/e943ec2bb48c6cbd693e0981d613… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Rename cloud download tool log dataset. Commit: 01a124314db553c2b9f646addc18aea3669905de https://github.com/galaxyproject/galaxy/commit/01a124314db553c2b9f646addc18… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py R tools/cloud/download.py R tools/cloud/download.xml A tools/cloud/send.py A tools/cloud/send.xml Log Message: ----------- Rename cloud/download.* to cloud/send.* Commit: b62e0476be4e27064efffd56a9516860a25e486e https://github.com/galaxyproject/galaxy/commit/b62e0476be4e27064efffd56a951… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/tools/__init__.py M tools/cloud/send.xml Log Message: ----------- cloud Download > Send refactoring in tool wrapper, & related places. Commit: 8f11f78aa2b9e1e342b03a7b3a8e3f47779eab12 https://github.com/galaxyproject/galaxy/commit/8f11f78aa2b9e1e342b03a7b3a8e… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M tools/cloud/send.py Log Message: ----------- download > send refactoring in the tool. Commit: d304068161dce41eba53a5ec2c4710a203fdf27a https://github.com/galaxyproject/galaxy/commit/d304068161dce41eba53a5ec2c47… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Cloud download > send refactoring in the related api. Commit: 24ed804ab40c931716c5f2f15b76f35160034c56 https://github.com/galaxyproject/galaxy/commit/24ed804ab40c931716c5f2f15b76… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Cloud download > send refactoring in cloud manager. Commit: a35b686dfda36439dd7bdfe632cefb242c383fac https://github.com/galaxyproject/galaxy/commit/a35b686dfda36439dd7bdfe632ce… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Assert if toolbox returns `send` tool before using it. Commit: 4e0b09499ec58cb90449ef15fb3fea424e58dd3f https://github.com/galaxyproject/galaxy/commit/4e0b09499ec58cb90449ef15fb3f… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M config/tool_conf.xml.main M config/tool_conf.xml.sample Log Message: ----------- Refactor cloud download > send in tool config. Commit: 47b41d1bb058244bcb06b88a5c612a4371d45e1f https://github.com/galaxyproject/galaxy/commit/47b41d1bb058244bcb06b88a5c61… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M tools/cloud/send.py Log Message: ----------- Add timestamp, and transfer ET & rate to the Send to cloud tool's log. Commit: b01ff7c2289bbfe7e6e9e543f0a98fd18f9a05f2 https://github.com/galaxyproject/galaxy/commit/b01ff7c2289bbfe7e6e9e543f0a9… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Log cloudauthz exceptions as `info`, not as an `exception`. Commit: b9771b7ccc417b9e4326151058f0fd221a21ff80 https://github.com/galaxyproject/galaxy/commit/b9771b7ccc417b9e4326151058f0… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Log entire cloudauthz exception, not just its message. Commit: 8543231b401bf3eec4d44d63f41c68e7b4ad8e02 https://github.com/galaxyproject/galaxy/commit/8543231b401bf3eec4d44d63f41c… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M tools/cloud/send.xml Log Message: ----------- Surround getting cloudauthz cred. in Send tool in a try-catch block. Commit: 8c95f174ba0d61c9632a03e9bec243509ca63a19 https://github.com/galaxyproject/galaxy/commit/8c95f174ba0d61c9632a03e9bec2… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M tools/cloud/send.py Log Message: ----------- Fix lint issues. Commit: d4d659a85191bbf8e7683c8840c716a96c09d85b https://github.com/galaxyproject/galaxy/commit/d4d659a85191bbf8e7683c8840c7… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M tools/cloud/send.xml Log Message: ----------- Replace the hardcoded msg with the exception msg in the cloud send tool. 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config/container_resolvers_conf.xml.sample M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/visualizations/scatterplot/package.json M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.css M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M doc/source/admin/galaxy_options.rst M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/interactive_environments.rst M doc/source/dev/index.rst M doc/source/dev/interactive_environments.rst A doc/source/releases/18.09.rst A doc/source/releases/18.09_announce.rst A doc/source/releases/19.01_announce.rst M lib/galaxy/authnz/managers.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/isa.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/cloud.py M lib/galaxy/managers/context.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py M lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py M lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py A lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/monitors.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/xml_util.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/pgcleanup.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M static/style/blue/base.css A static/style/blue/info_icon.svg M templates/admin/jobs.mako M templates/admin/review_tool_migration_stages.mako M templates/admin/tool_shed_repository/browse_repository.mako M templates/admin/tool_shed_repository/browse_tool_dependency.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/admin/tool_shed_repository/purge_repository_confirmation.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/admin/tool_shed_repository/view_workflow.mako M templates/message.mako M templates/user/info.mako M templates/user/register.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/history/share.mako A test-data/MTBLS6.zip M test/api/test_tools.py M test/api/test_tools_upload.py M test/base/populators.py A test/base/ssh_util.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml A test/functional/tools/remove_value.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigation.yml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py M test/unit/test_remote_shell.py M test/unit/tools/test_actions.py M tools/data_source/upload.py Log Message: ----------- Merge and resolve conflicts. Commit: a236c64ea79ac45ed8bcde67c586f16d92e7e70a https://github.com/galaxyproject/galaxy/commit/a236c64ea79ac45ed8bcde67c586… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M tools/cloud/send.xml Log Message: ----------- Repalce "sys.exc_info" with "Exception as e" in cloud Send tool wrapper. Commit: e30460049ff2ab7ec64b703fca590dab88db3ec7 https://github.com/galaxyproject/galaxy/commit/e30460049ff2ab7ec64b703fca59… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-28 (Sun, 28 Oct 2018) Changed paths: M tools/cloud/send.xml Log Message: ----------- Remove _ and capitalize each work in "overwrite_existing". Commit: ef70f20a58828b892e6af9b6b7515dbfd8f24e15 https://github.com/galaxyproject/galaxy/commit/ef70f20a58828b892e6af9b6b751… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-28 (Sun, 28 Oct 2018) Changed paths: M tools/cloud/send.xml Log Message: ----------- Swap authz_id and bucket; bucket is the first parameter now. Commit: 6f56ff10b9bc341fdaae879dec281e99fce6b1fc https://github.com/galaxyproject/galaxy/commit/6f56ff10b9bc341fdaae879dec28… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-28 (Sun, 28 Oct 2018) Changed paths: M tools/cloud/send.py Log Message: ----------- Remove `@` & msec from send tool timestamp. Commit: 39bdb67273700b0766250241801112a27dbc4b87 https://github.com/galaxyproject/galaxy/commit/39bdb67273700b07662502418011… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-28 (Sun, 28 Oct 2018) Changed paths: M tools/cloud/send.py Log Message: ----------- Make duplicate object timestamp shorter and use `_` instead of `-`. Commit: 7433e2640bc87fc76381eb7fcdcf07a1fde4671a https://github.com/galaxyproject/galaxy/commit/7433e2640bc87fc76381eb7fcdcf… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-28 (Sun, 28 Oct 2018) Changed paths: M tools/cloud/send.xml Log Message: ----------- Extend the help section and refactor `Authz` to `Cloud Authorization`. Commit: a71db8384cc512efd95c4ac89695d1584899874f https://github.com/galaxyproject/galaxy/commit/a71db8384cc512efd95c4ac89695… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Raise an exception in cloud get/send managers if OIDC is not enabled. Commit: 43e5a1828d2ba1ed11b7a5c7321fe075f06b9c0b https://github.com/galaxyproject/galaxy/commit/43e5a1828d2ba1ed11b7a5c7321f… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M tools/cloud/send.py Log Message: ----------- In Cloud send tool: surround error raising blocks of code in try-catch. Commit: 341f7d6372aa62bc6e84527925e0fb96622d1b84 https://github.com/galaxyproject/galaxy/commit/341f7d6372aa62bc6e84527925e0… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M tools/cloud/send.xml Log Message: ----------- Update output label & tool name to compose a more intuitive log label. Commit: 6c07a0370dadfdf0b9352c63b2d6f3357c33853d https://github.com/galaxyproject/galaxy/commit/6c07a0370dadfdf0b9352c63b2d6… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M tools/cloud/send.xml Log Message: ----------- Update description on send tool wrapper. Commit: 566ffaf9d549e3d1096db4996fc9133f133dee19 https://github.com/galaxyproject/galaxy/commit/566ffaf9d549e3d1096db4996fc9… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M tools/cloud/send.xml Log Message: ----------- Update send tool help text Commit: 2f2153292b39d3a2718c0950303f2b48b18838c9 https://github.com/galaxyproject/galaxy/commit/2f2153292b39d3a2718c0950303f… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M config/tool_conf.xml.main M config/tool_conf.xml.sample M lib/galaxy/authnz/managers.py M lib/galaxy/managers/cloud.py M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py A tools/cloud/send.py A tools/cloud/send.xml Log Message: ----------- Merge pull request #6583 from VJalili/cloud_download_tool Send data to cloud Compare: https://github.com/galaxyproject/galaxy/compare/eb57469eef96...2f2153292b39 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 37602f: Have Test load UCSC dbkeys from CVMFS
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 37602f74bf7b35e4dc4819db4bff287cd77ed916 https://github.com/galaxyproject/usegalaxy-playbook/commit/37602f74bf7b35e4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M env/test/files/galaxy/config/tool_data_table_conf.xml Log Message: ----------- Have Test load UCSC dbkeys from CVMFS **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] c42ea4: Fixed monitor Proxy set function
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c42ea4d9c5e38bc365b54d97f51c96def0f3def7 https://github.com/galaxyproject/galaxy/commit/c42ea4d9c5e38bc365b54d97f51c… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/onload/index.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/scripts/utils/installMonitor.js M client/webpack.config.js M client/yarn.lock Log Message: ----------- Fixed monitor Proxy set function Commit: 9b7b6ab04d4f0eaa6500cabacf632ef45acf5bcf https://github.com/galaxyproject/galaxy/commit/9b7b6ab04d4f0eaa6500cabacf63… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: A client/galaxy/scripts/libs/jquery.custom.js Log Message: ----------- Added jquery.custom.js to lib folder Commit: eb57469eef96f7225192128bd846237443e9b437 https://github.com/galaxyproject/galaxy/commit/eb57469eef96f7225192128bd846… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: A client/galaxy/scripts/libs/jquery.custom.js M client/galaxy/scripts/onload/index.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/scripts/utils/installMonitor.js M client/webpack.config.js M client/yarn.lock Log Message: ----------- Merge pull request #6970 from Nerdinacan/jquery_bundle Normalized jquery bundle Compare: https://github.com/galaxyproject/galaxy/compare/a4f21fca773c...eb57469eef96 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 443170: optimize images with optipng
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 443170e9128cd785dcfc24f73bddc5bcc1035fa3 https://github.com/galaxyproject/galaxy/commit/443170e9128cd785dcfc24f73bdd… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M client/galaxy/images/Armitagep_manhattan.png M client/galaxy/images/Armitagep_qqplot.png M client/galaxy/images/add_icon.png M client/galaxy/images/add_icon_dark.png M client/galaxy/images/aggregate_history1.png M client/galaxy/images/aggregate_history2.png M client/galaxy/images/bar_chart.png M client/galaxy/images/bed_warn.png M client/galaxy/images/closebox.png M client/galaxy/images/dat_points_table_brows_1.png M client/galaxy/images/data_empty.png M client/galaxy/images/data_error.png M client/galaxy/images/data_ok.png M client/galaxy/images/data_queued.png M client/galaxy/images/ddarrowsplit.png M client/galaxy/images/delete_tag_icon_gray.png M client/galaxy/images/delete_tag_icon_white.png M client/galaxy/images/documents-stack-faded.png M client/galaxy/images/dropdownarrow.png M client/galaxy/images/error_large.png M client/galaxy/images/error_small.png M client/galaxy/images/fetchTax.png M client/galaxy/images/form_body_bg.png M client/galaxy/images/fugue.png M client/galaxy/images/hatch-023858.png M client/galaxy/images/histogram.png M client/galaxy/images/histogram2.png M client/galaxy/images/history-buttons.png M client/galaxy/images/history-states.png M client/galaxy/images/info_large.png M client/galaxy/images/info_small.png M client/galaxy/images/kendall.png M client/galaxy/images/mag_glass.png M client/galaxy/images/masthead_bg.png M client/galaxy/images/mutation_visualization_example.png M client/galaxy/images/ok_large.png M client/galaxy/images/ok_small.png M client/galaxy/images/overview_arrows.png M client/galaxy/images/question-octagon-frame.png M client/galaxy/images/scatter.png M client/galaxy/images/scatterplot.png M client/galaxy/images/solid_qual.png M client/galaxy/images/sprite-fugue.png M client/galaxy/images/sprite-history-buttons.png M client/galaxy/images/sprite-history-states.png M client/galaxy/images/thumbtack_icon.png M client/galaxy/images/thumbtack_icon_dark.png M client/galaxy/images/wait_large.png M client/galaxy/images/wait_small.png Log Message: ----------- optimize images with optipng Commit: a4f21fca773c91032e11804e4a4c71646c213da0 https://github.com/galaxyproject/galaxy/commit/a4f21fca773c91032e11804e4a4c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M client/galaxy/images/Armitagep_manhattan.png M client/galaxy/images/Armitagep_qqplot.png M client/galaxy/images/add_icon.png M client/galaxy/images/add_icon_dark.png M client/galaxy/images/aggregate_history1.png M client/galaxy/images/aggregate_history2.png M client/galaxy/images/bar_chart.png M client/galaxy/images/bed_warn.png M client/galaxy/images/closebox.png M client/galaxy/images/dat_points_table_brows_1.png M client/galaxy/images/data_empty.png M client/galaxy/images/data_error.png M client/galaxy/images/data_ok.png M client/galaxy/images/data_queued.png M client/galaxy/images/ddarrowsplit.png M client/galaxy/images/delete_tag_icon_gray.png M client/galaxy/images/delete_tag_icon_white.png M client/galaxy/images/documents-stack-faded.png M client/galaxy/images/dropdownarrow.png M client/galaxy/images/error_large.png M client/galaxy/images/error_small.png M client/galaxy/images/fetchTax.png M client/galaxy/images/form_body_bg.png M client/galaxy/images/fugue.png M client/galaxy/images/hatch-023858.png M client/galaxy/images/histogram.png M client/galaxy/images/histogram2.png M client/galaxy/images/history-buttons.png M client/galaxy/images/history-states.png M client/galaxy/images/info_large.png M client/galaxy/images/info_small.png M client/galaxy/images/kendall.png M client/galaxy/images/mag_glass.png M client/galaxy/images/masthead_bg.png M client/galaxy/images/mutation_visualization_example.png M client/galaxy/images/ok_large.png M client/galaxy/images/ok_small.png M client/galaxy/images/overview_arrows.png M client/galaxy/images/question-octagon-frame.png M client/galaxy/images/scatter.png M client/galaxy/images/scatterplot.png M client/galaxy/images/solid_qual.png M client/galaxy/images/sprite-fugue.png M client/galaxy/images/sprite-history-buttons.png M client/galaxy/images/sprite-history-states.png M client/galaxy/images/thumbtack_icon.png M client/galaxy/images/thumbtack_icon_dark.png M client/galaxy/images/wait_large.png M client/galaxy/images/wait_small.png Log Message: ----------- Merge pull request #6980 from bgruening/optipng optimize images with optipng Compare: https://github.com/galaxyproject/galaxy/compare/b7c8bd47c907...a4f21fca773c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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